Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,986	C→T	*275* (TAG→TAA)	gadX ←	acid resistance regulon transcriptional activator, autoactivator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,986	0	C	T	100.0%	129.8 / NA	41	*275* (TAG→TAA)	gadX	acid resistance regulon transcriptional activator, autoactivator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/15);  total (26/15)

TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCA  >  NC_000913/3664851‑3665115                                                                                                                                        |                                                                                                                                  ttATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTtat                                                                                                                                <  1:668534/139‑1 (MQ=255)  tataTTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTtata                                                                                                                               <  1:585040/139‑1 (MQ=255)     atTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATc                                                                                                                            <  1:294898/139‑1 (MQ=255)            ttACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                     <  2:590326/139‑1 (MQ=255)                tGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttccttcc                                                                                                                 >  1:612298/1‑139 (MQ=255)                 gagaGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                     >  2:295760/1‑134 (MQ=255)                 gagaGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                     <  1:295760/134‑1 (MQ=255)                             tttCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    <  2:71305/139‑1 (MQ=255)                                 ccGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGcc                                                                                                >  2:572483/1‑139 (MQ=255)                                         aCAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAAt                                                                                        >  1:279215/1‑139 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCtt                                                                                  >  2:198122/1‑139 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCtt                                                                                  >  2:747036/1‑139 (MQ=255)                                                 tgtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                                >  1:114105/1‑139 (MQ=255)                                                  gtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                               >  2:628167/1‑139 (MQ=255)                                                     ataACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGcaa                                                                            <  1:628167/139‑1 (MQ=255)                                                            tttATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACt                                                                     >  1:87681/1‑139 (MQ=255)                                                                ttaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTgcc                                                                 >  1:765658/1‑139 (MQ=255)                                                                      tGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAg                                                           >  2:342750/1‑139 (MQ=255)                                                                        gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTg                                                                   <  2:764242/129‑1 (MQ=255)                                                                        gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTg                                                                   >  1:764242/1‑129 (MQ=255)                                                                        gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTc                                                         >  1:203916/1‑139 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGtt                                                   >  1:587066/1‑139 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGtt                                                   >  1:107510/1‑139 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                               <  2:87681/139‑1 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                               <  1:747036/139‑1 (MQ=255)                                                                                       ccTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAAtct                                          >  1:46929/1‑139 (MQ=255)                                                                                            tCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTgcg                                     >  1:204472/1‑139 (MQ=255)                                                                                            tCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTgcg                                     >  1:291078/1‑139 (MQ=255)                                                                                                ggTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTtat                                                                                                                                <  1:545553/44‑1 (MQ=255)                                                                                                ggTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTtat                                                                                                                                >  2:545553/1‑44 (MQ=255)                                                                                                ggTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                 >  1:416601/1‑139 (MQ=255)                                                                                                ggTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                 >  1:289616/1‑139 (MQ=255)                                                                                                     ccTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCt                            >  1:711196/1‑139 (MQ=255)                                                                                                              ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAAt                                            <  1:599139/114‑1 (MQ=255)                                                                                                              ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAAt                                            >  2:599139/1‑114 (MQ=255)                                                                                                              ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct                   >  1:477167/1‑139 (MQ=255)                                                                                                              ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct                   >  2:614848/1‑139 (MQ=255)                                                                                                                  ttttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCtgt               <  2:204472/139‑1 (MQ=255)                                                                                                                   tttttAGGTCTGAGTAAACCTTTATAATCTTATCCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCCCAACAATACTGGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCTTGATACTCtgtg              <  2:291078/139‑1 (MQ=255)                                                                                                                        aTGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt         <  1:614848/139‑1 (MQ=255)                                                                                                                               aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCa  >  1:99847/1‑139 (MQ=255)                                                                                                                                     aCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                               <  2:305467/104‑1 (MQ=255)                                                                                                                                        |                                                                                                                                  TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCA  >  NC_000913/3664851‑3665115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑